President Bush's torture policy has provoked perhaps the greatest schism between a president and the military in American history. From the outside, this battle royal over his abrogation of the Geneva conventions appears as a shadow war. But since the supreme court's ruling in Hamdan v Rumsfeld in June, deciding that Bush's kangaroo court commissions for detainees "violate both the UCMJ [Uniform Code of Military Justice] and the four Geneva conventions", the struggle has been forced into the open.

On September 6 Bush made his case for torture, offering as validity the interrogation under what he called an "alternative set of procedures" of an al-Qaida operative named Abu Zubaydah. Bush claimed he was a "senior terrorist leader" who "ran a terrorist camp" and had provided accurate information about planned terrorist attacks. In fact, Zubaydah was an al-Qaida travel agent (literally a travel agent), who, under torture, spun wild scenarios of terrorism that proved bogus. Zubaydah, it turns out, is a psychotic with the intelligence of a child. "This guy is insane, certifiable," said Dan Coleman, an FBI agent assigned to the al-Qaida taskforce.

Bush's argument for torture is partly based on the unstated premise that the more sadism, the more intelligence. While he referenced Zubaydah, he did not mention Jamal Ahmed al-Fadl, described by the FBI, according to the New Yorker, as "arguably the US's most valuable informant on al-Qaida", who is wined, dined and housed by the federal witness protection programme.

On September 15 the Senate armed services committee approved a bill affirming the Geneva conventions, sponsored by three Republicans with military backgrounds - John Warner, John McCain and Lindsey Graham. The former secretary of state Colin Powell, Bush's "good soldier," released a letter denouncing Bush's version. "The world," he wrote, "is beginning to doubt the moral basis of our fight against terrorism," and Bush's bill "would add to those doubts". That sentiment was underlined in another letter signed by 29 retired generals and CIA officials. General John Batiste, former commander of the 1st army division in Iraq, appeared on CNN to scourge the administration's policy as "unlawful", "wrong", and responsible for Abu Ghraib.

Before the committee vote, Bush's administration had tried to coerce the top military lawyers, the judge advocates general (JAGs), into signing a statement of uncritical support, which they refused to do. The Republican senators opposing Bush's torture policy first learned about the military's profound opposition from the JAGs. For years, the administration has considered them subversive and tried to eliminate them as a separate corps and substitute neoconservative political appointees.

In the summer of 2004 General Thomas J Fiscus, the top air force JAG, informed the senators that the administration's assertion that the JAGs backed Bush on torture was utterly false. Suspicion instantly fell upon Fiscus, one of the most aggressive opponents of torture policy, as the senators' source. Within weeks he was drummed out under a cloud of anonymous allegations by Pentagon officials of "improper relations" with women. His discharge was trumpeted in the press, but his role in the torture debate remained unknown.

Bush had intended to use his post-Hamdan bill to taint the Democrats, but instead he has split his party and further antagonised the military. His standoff on torture threatens to leave no policy whatsoever, and leave his war on terror in a twilight zone beyond the rule of law.

· Sidney Blumenthal is a former senior adviser to President Clinton. To buy his book, How Bush Rules, for £16.95 plus p&p call 0870 836 0749 or visit www.guardianbookshop.co.uk